##gff-version 3
##sequence-region NC_013132 1 13159
# conversion-by bp_genbank2gff3.pl
# organism Chitinophaga pinensis DSM 2588
# Note Chitinophaga pinensis DSM 2588, complete genome.
# date 26-AUG-2019
NC_013132	GenBank	region	1	13159	.	+	1	ID=NC_013132;Dbxref=BioProject:PRJNA224116,taxon:485918;Name=NC_013132;Note=Chitinophaga pinensis DSM 2588%2C complete genome.,REFSEQ INFORMATION: The reference sequence was derived from CP001699. URL -- http://www.jgi.doe.gov JGI Project ID: 4082984 Source DNA and organism available from Hans-Peter Klenk at the German Collection of Microorganisms and Cell Cultures (DSMZ) (hans-peter.klenk@dsmz.de) Contacts: Jonathan A. Eisen (jaeisen@ucdavis.edu) David Bruce (microbe@cuba.jgi-psf.org) Whole genome sequencing and draft assembly at JGI-PGF Finishing done by JGI-LANL Annotation by JGI-ORNL and JGI-PGF The JGI and collaborators endorse the principles for the distribution and use of large scale sequencing data adopted by the larger genome sequencing community and urge users of this data to follow them. It is our intention to publish the work of this project in a timely fashion and we welcome collaborative interaction on the project and analysis. (http://www.genome.gov/page.cfm?pageID%3D10506376). The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ ##Genome-Annotation-Data-START## Annotation Provider :: NCBI RefSeq Annotation Date :: 08/26/2019 00:28:39 Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method :: Best-placed reference protein set,GeneMarkS-2+ Annotation Software revision :: 4.9 Features Annotated :: Gene,CDS,rRNA,tRNA,ncRNA,repeat_region Genes (total) :: 7,171 CDSs (total) :: 7,077 Genes (coding) :: 7,009 CDSs (with protein) :: 7,009 Genes (RNA) :: 94 rRNAs :: 6,6,6 (5S,16S,23S) complete rRNAs :: 6,6,6 (5S,16S,23S) tRNAs :: 73 ncRNAs :: 3 Pseudo Genes (total) :: 68 CDSs (without protein) :: 68 Pseudo Genes (ambiguous residues) :: 0 of 68 Pseudo Genes (frameshifted) :: 19 of 68 Pseudo Genes (incomplete) :: 47 of 68 Pseudo Genes (internal stop) :: 11 of 68 Pseudo Genes (multiple problems) :: 8 of 68 ##Genome-Annotation-Data-END## ##Metadata-START## Organism Display Name :: Chitinophaga pinensis UQM 2034,DSM 2588 Culture Collection ID :: DSM 2588,ATCC 43595,LMG 13176,UQM 2034 GOLD Stamp ID :: Gi02244 Funding Program :: DOE-GEBA 2007 Gene Calling Method :: Prodigal Isolation Site :: Pine litter in Australia Isolation Country :: Australia Oxygen Requirement :: Aerobe Cell Shape :: Rod-shaped Motility :: Motile Sporulation :: Nonsporulating Temperature Range :: Mesophile Temperature Optimum :: 23 - 24C pH :: 7 Gram Staining :: gram- Biotic Relationship :: Free living Diseases :: None Phenotypes :: Biomass degrader,Chitin degradation Energy Source :: Chemoorganotroph ##Metadata-END## COMPLETENESS: full length. ,type strain of Chitinophaga pinensis;comment1=REFSEQ INFORMATION: The reference sequence was derived from CP001699. URL -- http://www.jgi.doe.gov JGI Project ID: 4082984 Source DNA and organism available from Hans-Peter Klenk at the German Collection of Microorganisms and Cell Cultures (DSMZ) (hans-peter.klenk@dsmz.de) Contacts: Jonathan A. Eisen (jaeisen@ucdavis.edu) David Bruce (microbe@cuba.jgi-psf.org) Whole genome sequencing and draft assembly at JGI-PGF Finishing done by JGI-LANL Annotation by JGI-ORNL and JGI-PGF The JGI and collaborators endorse the principles for the distribution and use of large scale sequencing data adopted by the larger genome sequencing community and urge users of this data to follow them. It is our intention to publish the work of this project in a timely fashion and we welcome collaborative interaction on the project and analysis. (http://www.genome.gov/page.cfm?pageID%3D10506376). The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ ##Genome-Annotation-Data-START## Annotation Provider :: NCBI RefSeq Annotation Date :: 08/26/2019 00:28:39 Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method :: Best-placed reference protein set%3B GeneMarkS-2+ Annotation Software revision :: 4.9 Features Annotated :: Gene%3B CDS%3B rRNA%3B tRNA%3B ncRNA%3B repeat_region Genes (total) :: 7%2C171 CDSs (total) :: 7%2C077 Genes (coding) :: 7%2C009 CDSs (with protein) :: 7%2C009 Genes (RNA) :: 94 rRNAs :: 6%2C 6%2C 6 (5S%2C 16S%2C 23S) complete rRNAs :: 6%2C 6%2C 6 (5S%2C 16S%2C 23S) tRNAs :: 73 ncRNAs :: 3 Pseudo Genes (total) :: 68 CDSs (without protein) :: 68 Pseudo Genes (ambiguous residues) :: 0 of 68 Pseudo Genes (frameshifted) :: 19 of 68 Pseudo Genes (incomplete) :: 47 of 68 Pseudo Genes (internal stop) :: 11 of 68 Pseudo Genes (multiple problems) :: 8 of 68 ##Genome-Annotation-Data-END## ##Metadata-START## Organism Display Name :: Chitinophaga pinensis UQM 2034%2C DSM 2588 Culture Collection ID :: DSM 2588%2C ATCC 43595%2C LMG 13176%2C UQM 2034 GOLD Stamp ID :: Gi02244 Funding Program :: DOE-GEBA 2007 Gene Calling Method :: Prodigal Isolation Site :: Pine litter in Australia Isolation Country :: Australia Oxygen Requirement :: Aerobe Cell Shape :: Rod-shaped Motility :: Motile Sporulation :: Nonsporulating Temperature Range :: Mesophile Temperature Optimum :: 23 - 24C pH :: 7 Gram Staining :: gram- Biotic Relationship :: Free living Diseases :: None Phenotypes :: Biomass degrader%2C Chitin degradation Energy Source :: Chemoorganotroph ##Metadata-END## COMPLETENESS: full length. ;date=26-AUG-2019;mol_type=genomic DNA;organism=Chitinophaga pinensis DSM 2588;strain=DSM 2588;type_material=type strain of Chitinophaga pinensis
NC_013132	GenBank	gene	1	870	.	-	1	ID=CPIN_RS31475;Name=CPIN_RS31475;old_locus_tag=Cpin_6364
NC_013132	GenBank	mRNA	1	870	.	-	1	ID=CPIN_RS31475.t01;Parent=CPIN_RS31475
NC_013132	GenBank	CDS	1	870	.	-	1	ID=CPIN_RS31475.p01;Parent=CPIN_RS31475.t01;Name=CPIN_RS31475;Note=Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.;codon_start=1;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;old_locus_tag=Cpin_6364;product=hypothetical protein;protein_id=WP_012793932.1;transl_table=11;translation=length.289
NC_013132	GenBank	exon	1	870	.	-	1	Parent=CPIN_RS31475.t01
NC_013132	GenBank	gene	908	2647	.	-	1	ID=CPIN_RS31480;Name=CPIN_RS31480;old_locus_tag=Cpin_6365
NC_013132	GenBank	mRNA	908	2647	.	-	1	ID=CPIN_RS31480.t01;Parent=CPIN_RS31480
NC_013132	GenBank	CDS	908	2647	.	-	1	ID=CPIN_RS31480.p01;Parent=CPIN_RS31480.t01;Name=CPIN_RS31480;Note=Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.;codon_start=1;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;old_locus_tag=Cpin_6365;product=hypothetical protein;protein_id=WP_012793933.1;transl_table=11;translation=length.579
NC_013132	GenBank	exon	908	2647	.	-	1	Parent=CPIN_RS31480.t01
NC_013132	GenBank	gene	2723	3982	.	-	1	ID=CPIN_RS31485;Name=CPIN_RS31485;old_locus_tag=Cpin_6366
NC_013132	GenBank	mRNA	2723	3982	.	-	1	ID=CPIN_RS31485.t01;Parent=CPIN_RS31485
NC_013132	GenBank	CDS	2723	3982	.	-	1	ID=CPIN_RS31485.p01;Parent=CPIN_RS31485.t01;Name=CPIN_RS31485;Note=Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.;codon_start=1;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;old_locus_tag=Cpin_6366;product=hypothetical protein;protein_id=WP_012793934.1;transl_table=11;translation=length.419
NC_013132	GenBank	exon	2723	3982	.	-	1	Parent=CPIN_RS31485.t01
NC_013132	GenBank	gene	3999	5642	.	-	1	ID=CPIN_RS31490;Name=CPIN_RS31490;old_locus_tag=Cpin_6367
NC_013132	GenBank	mRNA	3999	5642	.	-	1	ID=CPIN_RS31490.t01;Parent=CPIN_RS31490
NC_013132	GenBank	CDS	3999	5642	.	-	1	ID=CPIN_RS31490.p01;Parent=CPIN_RS31490.t01;Name=CPIN_RS31490;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_009279815.1;old_locus_tag=Cpin_6367;product=RagB/SusD family nutrient uptake outer membrane protein;protein_id=WP_012793935.1;transl_table=11;translation=length.547
NC_013132	GenBank	exon	3999	5642	.	-	1	Parent=CPIN_RS31490.t01
NC_013132	GenBank	gene	5663	8860	.	-	1	ID=CPIN_RS31495;Name=CPIN_RS31495;old_locus_tag=Cpin_6368
NC_013132	GenBank	mRNA	5663	8860	.	-	1	ID=CPIN_RS31495.t01;Parent=CPIN_RS31495
NC_013132	GenBank	CDS	5663	8860	.	-	1	ID=CPIN_RS31495.p01;Parent=CPIN_RS31495.t01;Name=CPIN_RS31495;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: protein motif:HMM:TIGR04056.1;old_locus_tag=Cpin_6368;product=TonB-dependent receptor;protein_id=WP_012793936.1;transl_table=11;translation=length.1065
NC_013132	GenBank	exon	5663	8860	.	-	1	Parent=CPIN_RS31495.t01
NC_013132	GenBank	gene	9059	13159	.	-	1	ID=CPIN_RS31500;Name=CPIN_RS31500;old_locus_tag=Cpin_6369
NC_013132	GenBank	mRNA	9059	13159	.	-	1	ID=CPIN_RS31500.t01;Parent=CPIN_RS31500
NC_013132	GenBank	CDS	9059	13159	.	-	1	ID=CPIN_RS31500.p01;Parent=CPIN_RS31500.t01;Name=CPIN_RS31500;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_014218988.1;old_locus_tag=Cpin_6369;product=hybrid sensor histidine kinase/response regulator transcription factor;protein_id=WP_012793937.1;transl_table=11;translation=length.1366
NC_013132	GenBank	exon	9059	13159	.	-	1	Parent=CPIN_RS31500.t01